RT Journal Article
SR Electronic
T1 Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree
JF Genetics
JO Genetics
FD Genetics Society of America
SP 791
OP 805
DO 10.1534/genetics.117.300401
VO 208
IS 2
A1 Yang, Zongfeng
A1 Li, Junrui
A1 Wiehe, Thomas
A1 Li, Haipeng
YR 2018
UL http://www.genetics.org/content/208/2/791.abstract
AB Many population genomic studies have been conducted in the past to search for traces of recent events of positive selection. These traces, however, can be obscured by temporal variation of population size or other demographic factors. To reduce the confounding impact of demography, the coalescent tree topology has been used as an additional source of information for detecting recent positive selection in a population or a species. Based on the branching pattern at the root, we partition the hypothetical coalescent tree, inferred from a sequence sample, into two subtrees. The reasoning is that positive selection could impose a strong impact on branch length in one of the two subtrees while demography has the same effect on average on both subtrees. Thus, positive selection should be detectable by comparing statistics calculated for the two subtrees. Simulations demonstrate that the proposed test based on these principles has high power to detect recent positive selection even when DNA polymorphism data from only one locus is available, and that it is robust to the confounding effect of demography. One feature is that all components in the summary statistics () can be computed analytically. Moreover, misinference of derived and ancestral alleles is seen to have only a limited effect on the test, and it therefore avoids a notorious problem when searching for traces of recent positive selection.